Interpretive Summary: This manuscript describes the sequencing and analysis of the pig genome and its comparison with the genome of sequences of other wild and domestic pigs from Europe and Asia. Our efforts, as part of an international consortium, resulted in the manual annotation of over 1,400 genes to provide a basic description of the pig immunome i.e., the portion of the genome devoted to the immune response. We also conducted a large-scale comparative assessment of the pig, mouse, bovine and human genomes focusing on shared and unique gene families involved in immunity and inflammation. This analysis revealed an overwhelming similarity of pigs to humans compared to mice and cows for most parameters evaluated thus validating their use as a useful biomedical model. It also identified cow and pig-specific expansion of certain gene families. These efforts will contribute significantly toward promoting human and swine health.

Technical Abstract:
For nearly 8,000 years pigs and humans have shared a close and complex relationship, and through domestication and breeding, humans have shaped the genomes of current diverse pig breeds. Here we present the assembly and analysis of the genome sequence of a female domestic pig from the European Duroc breed and its comparison with the genome of sequences of other wild and domestic pigs from Europe and Asia. Pigs (Sus scrofa) emerged in Southeast Asia and subsequently spread across most of Eurasia. Our sequence results show a deep phylogenetic split between European and Asian wild boars that occurred around 1 million years ago. We identified fixed differences at over 1,700 amino- acids positions in almost 1,200 different genes and a selective sweep analysis indicated strong selection on genes involved in RNA processing and regulation. A comparison with other mammals demonstrated the rapid evolution of immune related and olfactory receptor encoding genes. Rapid gene expansions were observed for the cathelicidin, type I interferon and olfactory gene families. Pig, together with the rat, has the largest repertoire of functional olfactory receptor genes seen in any other species reflecting the importance of smell in this scavenging animal. For millennia the pig has served as an important source for animal protein for human nutrition, but more recently because of its similar physiology to humans, it has also become an important biomedical animal model. The pig genome sequence provides an important resource for further improvements of this important livestock species and our identification of many putative disease-causing variants in the porcine genome extends the potential of the pig as a biomedical model. Supported by funds from ARS Project Plans 1235-51000-055-00D and 1265-32000-098-00D and BARC summer student fellowships.